Note that str_replace can accept an array of values as the needle. For example,

$body = str_replace(array(',', '.'), '', $body);

replaces any instance of an element in the array with an empty string.

Alternatively, I'd suggest looking at some pre-built search and indexing libraries. It's a very hard area to get right from scratch and you're much more likely to get reliable results using an already-polished indexing and searching algorithm.